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Creators/Authors contains: "Kelley, James"

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  1. Abstract BackgroundCombined impacts from anthropogenic pressures and climate change threaten coastal ecosystems and their capacity to protect communities from hazards. One approach towards improving coastal protection is to implement “nature-based solutions” (NBS), which are actions working with nature to benefit nature and humans. Despite recent increases in global implementation of NBS projects for coastal protection, substantial gaps exist in our understanding of NBS performance. To help fill this gap, we systematically mapped the global evidence base on the ecological, physical, economic, and social performance of NBS interventions related to coastal protection. We focused on active NBS interventions, such as restoring or creating habitat, adding structure, or modifying sediment in six shallow biogenic ecosystems: salt marsh, seagrass, kelp forest, mangrove, coral reef, and shellfish reef. MethodsWe identified potentially relevant articles on the performance of NBS for coastal protection using predefined and tested search strategies across two indexing platforms, one bibliographic database, two open discovery citation indexes, one web-based search engine, and a novel literature discovery tool. We also searched 45 organizational websites for literature and solicited literature from 66 subject matter experts. Potentially relevant articles were deduplicated and then screened by title and abstract with assistance from a machine learning algorithm. Following title and abstract screening, we conducted full text screening, extracted relevant metadata into a predefined codebook, and analyzed the evidence base to determine the distribution and abundance of evidence and answer our research questions on NBS performance. ResultsOur search captured > 37,000 articles, of which 252 met our eligibility criteria for relevance to NBS performance for coastal protection and were included in the systematic map. Evidence stemmed from 31 countries and increased from the 1980s through the 2020s. Active NBS interventions for coastal protection were most often implemented in salt marshes (45%), mangrove forests (26%), and shellfish reefs (20%), whereas there were fewer NBS studies in seagrass meadows (4%), coral reefs (4%), or kelp beds (< 1%). Performance evaluations of NBS were typically conducted using observational or experimental methods at local spatial scales and over short temporal scales (< 1 year to 5 years). Evidence clusters existed for several types of NBS interventions, including restoration and addition of structures (e.g., those consisting of artificial, hybrid, or natural materials), yet evidence gaps existed for NBS interventions like alteration of invasive species. Evaluations of NBS performance commonly focused on ecological (e.g., species and population, habitat, community) and physical (e.g., waves, sediment and morphology) outcomes, whereas pronounced evidence gaps existed for economic (e.g., living standards, capital) and social (e.g., basic infrastructure, health) outcomes. ConclusionsThis systematic map highlights evidence clusters and evidence gaps related to the performance of active NBS interventions for coastal protection in shallow, biogenic ecosystems. The synthesized evidence base will help guide future research and management of NBS for coastal protection so that active interventions can be designed, sited, constructed, monitored, and adaptively managed to maximize co-benefits. Promising avenues for future research and management initiatives include implementing broad-scale spatial and temporal monitoring of NBS in multidisciplinary teams to examine not only ecological and physical outcomes but also economic and social outcomes, as well as conducting further synthesis on evidence clusters that may reveal measures of effect for specific NBS interventions. Since NBS can deliver multiple benefits, measuring a diverse suite of response variables, especially those related to ecosystem function, as well as social and economic responses, may help justify and improve societal benefits of NBS. Such an approach can help ensure that NBS can be strategically harnessed and managed to meet coastal protection goals and provide co-benefits for nature and people. 
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  2. SARSNTdb offers a curated, nucleotide-centric database for users of varying levels of SARS-CoV-2 knowledge. Its user-friendly interface enables querying coding regions and coordinate intervals to find out the various functional and selective constraints that act upon the corresponding nucleotides and amino acids. Users can easily obtain information about viral genes and proteins, functional domains, repeats, secondary structure formation, intragenomic interactions, and mutation prevalence. Currently, many databases are focused on the phylogeny and amino acid substitutions, mainly in the spike protein. We took a novel, more nucleotide-focused approach as RNA does more than just code for proteins and many insights can be gleaned from its study. For example, RNA-targeted drug therapies for SARS-CoV-2 are currently being developed and it is essential to understand the features only visible at that level. This database enables the user to identify regions that are more prone to forming secondary structures that drugs can target. SARSNTdb also provides illustrative mutation data from a subset of ~25,000 patient samples with a reliable read coverage across the whole genome (from different locations and time points in the pandemic. Finally, the database allows for comparing SARS-CoV-2 and SARS-CoV domains and sequences. SARSNTdb can serve the research community by being a curated repository for information that gives a jump start to analyze a mutation’s effect far beyond just determining synonymous/non-synonymous substitutions in protein sequences. 
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